1WK4 | pdb_00001wk4

Crystal structure of ttk003001606

• PDB DOI: https://doi.org/10.2210/pdb1WK4/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-05-30 Released: 2004-11-30 
• Deposition Author(s): Kaminishi, T., Sakai, H., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.275 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal structure of ttk003001606

Kaminishi, T., Sakai, H., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.14 kDa 
• Atom Count: 4,299 
• Modeled Residue Count: 522 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ttk003001606	A, B, C	174	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ05 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ05  Go to UniProtKB:  Q5SJ05

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	D [auth A], E [auth B], F [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.275 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.332	α = 90
b = 78.332	β = 90
c = 197.038	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-30 
Deposition Author(s): Kaminishi, T., Sakai, H., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-11-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary